Related literature
For the room-temperature, disordered structure of tetrahydropyrimidin-2(1H)-one, see: Calogero et al. (1980).
Experimental
Crystal data
C4H8N2O Mr = 100.12 Orthorhombic, P n m a a = 9.9958 (1) Å b = 7.1327 (1) Å c = 6.7365 (1) Å V = 480.29 (1) Å3 Z = 4 Mo Kα radiation μ = 0.10 mm−1 T = 100 (2) K 0.35 × 0.20 × 0.15 mm
|
Data collection
Bruker SMART APEX diffractometer Absorption correction: none 6595 measured reflections 749 independent reflections 719 reflections with I > 2σ(I) Rint = 0.020
|
D—H⋯A | D—H | H⋯A | D⋯A | D—H⋯A | N1—H1⋯O1i | 0.89 (1) | 1.97 (1) | 2.864 (1) | 178 (1) | Symmetry code: (i) -x+1, -y+1, -z+1. | |
Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: X-SEED (Barbour, 2001); software used to prepare material for publication: publCIF (Westrip, 2008).
Supporting information
The commercially available compound was crystalline. A large block was cut into a smaller specimen.
All hydrogen atoms were located in a difference Fourier map, and were freely refined.
Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: X-SEED (Barbour, 2001); software used to prepare material for publication: publCIF (Westrip, 2008).
3,4,5,6-tetrahydropyrimidin-2(1
H)-one
top Crystal data top C4H8N2O | F(000) = 216 |
Mr = 100.12 | Dx = 1.385 Mg m−3 |
Orthorhombic, Pnma | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ac 2n | Cell parameters from 4972 reflections |
a = 9.9958 (1) Å | θ = 3.0–30.4° |
b = 7.1327 (1) Å | µ = 0.10 mm−1 |
c = 6.7365 (1) Å | T = 100 K |
V = 480.29 (1) Å3 | Block, colorless |
Z = 4 | 0.35 × 0.20 × 0.15 mm |
Data collection top Bruker SMART APEXII diffractometer | 719 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.020 |
Graphite monochromator | θmax = 30.0°, θmin = 3.7° |
ϕ and ω scans | h = −12→13 |
6595 measured reflections | k = −9→10 |
749 independent reflections | l = −9→9 |
Refinement top Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.036 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.110 | All H-atom parameters refined |
S = 1.06 | w = 1/[σ2(Fo2) + (0.0818P)2 + 0.084P] where P = (Fo2 + 2Fc2)/3 |
749 reflections | (Δ/σ)max = 0.001 |
55 parameters | Δρmax = 0.49 e Å−3 |
0 restraints | Δρmin = −0.22 e Å−3 |
Crystal data top C4H8N2O | V = 480.29 (1) Å3 |
Mr = 100.12 | Z = 4 |
Orthorhombic, Pnma | Mo Kα radiation |
a = 9.9958 (1) Å | µ = 0.10 mm−1 |
b = 7.1327 (1) Å | T = 100 K |
c = 6.7365 (1) Å | 0.35 × 0.20 × 0.15 mm |
Data collection top Bruker SMART APEXII diffractometer | 719 reflections with I > 2σ(I) |
6595 measured reflections | Rint = 0.020 |
749 independent reflections | |
Refinement top R[F2 > 2σ(F2)] = 0.036 | 0 restraints |
wR(F2) = 0.110 | All H-atom parameters refined |
S = 1.06 | Δρmax = 0.49 e Å−3 |
749 reflections | Δρmin = −0.22 e Å−3 |
55 parameters | |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
O1 | 0.48291 (8) | 0.7500 | 0.51927 (11) | 0.0143 (2) | |
N1 | 0.58480 (7) | 0.58713 (8) | 0.27287 (9) | 0.0140 (2) | |
C1 | 0.54996 (10) | 0.7500 | 0.36064 (14) | 0.0113 (2) | |
C2 | 0.67121 (7) | 0.57605 (10) | 0.09858 (11) | 0.0145 (2) | |
C3 | 0.65258 (11) | 0.7500 | −0.02874 (14) | 0.0146 (3) | |
H1 | 0.5642 (13) | 0.4836 (18) | 0.3405 (19) | 0.023 (3)* | |
H21 | 0.6483 (11) | 0.4643 (17) | 0.0232 (17) | 0.017 (3)* | |
H22 | 0.7668 (11) | 0.5621 (17) | 0.1397 (17) | 0.017 (2)* | |
H31 | 0.5609 (18) | 0.7500 | −0.089 (3) | 0.023 (4)* | |
H32 | 0.7163 (18) | 0.7500 | −0.140 (3) | 0.023 (4)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O1 | 0.0176 (4) | 0.0122 (4) | 0.0132 (4) | 0.000 | 0.0045 (3) | 0.000 |
N1 | 0.0188 (4) | 0.0099 (3) | 0.0133 (3) | 0.0003 (2) | 0.0047 (2) | 0.00012 (19) |
C1 | 0.0109 (4) | 0.0111 (5) | 0.0118 (4) | 0.000 | −0.0008 (3) | 0.000 |
C2 | 0.0173 (4) | 0.0128 (4) | 0.0133 (4) | 0.0010 (2) | 0.0039 (2) | −0.0008 (2) |
C3 | 0.0177 (5) | 0.0145 (5) | 0.0117 (4) | 0.000 | 0.0013 (3) | 0.000 |
Geometric parameters (Å, º) top O1—C1 | 1.2614 (12) | C2—H21 | 0.972 (12) |
N1—C1 | 1.3492 (8) | C2—H22 | 1.000 (11) |
N1—C2 | 1.4597 (9) | C3—C2i | 1.5198 (9) |
N1—H1 | 0.892 (13) | C3—H31 | 1.001 (18) |
C1—N1i | 1.3492 (8) | C3—H32 | 0.982 (19) |
C2—C3 | 1.5198 (9) | | |
| | | |
C1—N1—C2 | 123.49 (6) | N1—C2—H22 | 110.4 (7) |
C1—N1—H1 | 115.4 (8) | C3—C2—H22 | 110.8 (7) |
C2—N1—H1 | 120.2 (8) | H21—C2—H22 | 106.8 (10) |
O1—C1—N1 | 120.56 (4) | C2i—C3—C2 | 109.45 (8) |
O1—C1—N1i | 120.56 (4) | C2i—C3—H31 | 109.9 (5) |
N1—C1—N1i | 118.86 (9) | C2—C3—H31 | 109.9 (5) |
N1—C2—C3 | 109.71 (6) | C2i—C3—H32 | 110.5 (5) |
N1—C2—H21 | 109.0 (7) | C2—C3—H32 | 110.5 (5) |
C3—C2—H21 | 110.2 (7) | H31—C3—H32 | 106.7 (15) |
| | | |
C2—N1—C1—O1 | −174.85 (8) | C1—N1—C2—C3 | −30.95 (10) |
C2—N1—C1—N1i | 7.00 (14) | N1—C2—C3—C2i | 52.71 (10) |
Symmetry code: (i) x, −y+3/2, z. |
Hydrogen-bond geometry (Å, º) top D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O1ii | 0.89 (1) | 1.97 (1) | 2.864 (1) | 178 (1) |
Symmetry code: (ii) −x+1, −y+1, −z+1. |
Experimental details
Crystal data |
Chemical formula | C4H8N2O |
Mr | 100.12 |
Crystal system, space group | Orthorhombic, Pnma |
Temperature (K) | 100 |
a, b, c (Å) | 9.9958 (1), 7.1327 (1), 6.7365 (1) |
V (Å3) | 480.29 (1) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.10 |
Crystal size (mm) | 0.35 × 0.20 × 0.15 |
|
Data collection |
Diffractometer | Bruker SMART APEXII diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 6595, 749, 719 |
Rint | 0.020 |
(sin θ/λ)max (Å−1) | 0.703 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.036, 0.110, 1.06 |
No. of reflections | 749 |
No. of parameters | 55 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.49, −0.22 |
Hydrogen-bond geometry (Å, º) top D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O1i | 0.89 (1) | 1.97 (1) | 2.864 (1) | 178 (1) |
Symmetry code: (i) −x+1, −y+1, −z+1. |
Acknowledgements
We thank the University of Malaya for the purchase of the diffractometer.
References
Barbour, L. J. (2001). J. Supramol. Chem. 1, 189–191. CrossRef CAS Google Scholar
Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Calogero, S., Russo, U. & Del Pra, A. (1980). J. Chem. Soc. Dalton Trans. pp. 646–653. CSD CrossRef Web of Science Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Westrip, S. P. (2008). publCIF. In preparation. Google Scholar
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ISSN: 2056-9890
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access
The crystal structure of tetrahydropyrimidin-2(1H)-one (Scheme I) was refined as a disorder model, the second of the three methylene carbon atoms being disordered about a mirror plane by a ratio of 0.7:0.3 (Calogero et al., 1980). However, the structure is ordered at low temperature (Fig. 1); adjacent molecules are linked by a N–H···O hydrogen bond into a chain motif.